Tag: GIAB

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

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iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

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GIAB Benchmark (High Confidence) Bed Filles

GIAB Benchmark (High Confidence) Bed Filles 0 Hi all, I havent used Genome in a Bottle for a couple of years. When I did use it, I recall I would download samples in VCF format for: AshkenaziTrio (three each) NA12878 (only one) ChineseTrio (three each) I would then download what…

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qualimap2 mean mapping quality

qualimap2 mean mapping quality 0 I’ve done a contrast experiment to see the difference between the bam with BQSR and the bam without BQSR. I use qualimap to evaluate both bams. This is the confusing part. Using hap.py and the giab na12878 truth vcf, shows the bam with BQSR is…

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